chr6-88168233-G-A

Variant names:

• chr6-88168233-G-A
• rs2180619
• ENST00000756364.1:n.128+42636G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000756364.1(ENSG00000298549):​n.128+42636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,944 control chromosomes in the GnomAD database, including 22,341 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (22341 hom., cov: 31)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 46 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756364.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298549	ENST00000756364.1		n.128+42636G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80810 AN: 151826 Hom.: 22338 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.622

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.562

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.532 AC: 80849 AN: 151944 Hom.: 22341 Cov.: 31 AF XY: 0.534 AC XY: 39643 AN XY: 74250

African (AFR) AF: 0.374 AC: 15483 AN: 41414

American (AMR) AF: 0.535 AC: 8180 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3470

East Asian (EAS) AF: 0.774 AC: 3993 AN: 5158

South Asian (SAS) AF: 0.594 AC: 2861 AN: 4814

European-Finnish (FIN) AF: 0.523 AC: 5530 AN: 10564

Middle Eastern (MID) AF: 0.631 AC: 183 AN: 290

European-Non Finnish (NFE) AF: 0.605 AC: 41100 AN: 67936

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.581 Hom.: 95908

Bravo AF: 0.526

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.34
DANN	Benign	0.75
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2180619; hg19: chr6-88877952;